[mira_talk] Re: MIRA and .abi files

  • From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 23 Oct 2009 23:28:08 +0200

Hi Alessandro,

it's not just to extract sequences/qualities from the abi files, they
usually contain vector and low quality sequences. You need to take care to
remove these from your data.

You could basecall your abi data using phred(1) or TraceTuner(2) basecaller
and subsequently clip the data using lucy(3) or something similar.

You could also use Staden's pre-gap4(4) which is a complete preprocessing
solution for sanger data
(though I wouldn't feed it with 500,000 sanger reads ;-).


(1) = http://www.phrap.org/phredphrapconsed.html
(2) = http://sourceforge.net/projects/tracetuner/
(3) = http://sourceforge.net/projects/lucy/
(4) = http://staden.sourceforge.net/

2009/10/23 Alessandro Riccombeni <rikkomba@xxxxxxxxx>

> HI,
> I am a newbie PhD student. I just started using MIRA, and I have to try
> making a hybrid 454-Sanger assembly. MIRA is run on a Linux server.
> I tried MIRA with 454 data only until now. The Sanger data I have been
> given include .fas and .abi files. THat means, I have the fasta sequences
> for both forward and reverse primers, but I should get the qualities from
> the .abi files. I couldn't find, until now, a fast way to extract the
> quality info I need for MIRA from these .abi files. Can anybody direct me to
> some online resource? THanks for your help,
> Alessandro R.

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